Phylogenetics: finding out how genes and species are related

How do evolutionary biologists look into the past? How can we know when and where an organism has lived, if it left no fossils (like most butterflies)? How can we tell if genes were exchanged between species?

All these questions are studied by a field of biology called phylogenetics, from the Greek phyle=kind and genesis=origin.

Reconstructing the tree of life

Our understanding of the evolution of butterflies and other forms of life rests on the knowledge of how species are related to each other. These relations are often depicted as a tree, where the tips of branches are species, and connections between them represent ancient ancestors. These relations can be inferred from DNA sequences. Some mutations in DNA are not purged and accumulate with time at steady rate. If we compare the same gene from two butterfly species, we are likely to find some differences: the more variation, the more time must have passed since the two organisms had a common ancestor. For instance, the genomic sequences from humans and chimpanzees differ a lot less than those from humans and macaques, illustrating our closer evolutionary affinity to chimps.

Figure 1. An alignment of the 16S gene from four species of butterflies. The three South American Heliconius are more similar to each other than they are to the African Acraea, reflecting evolutionary history.

Figure 2. The phylogenetic tree of Heliconius and relatives. Using the molecular clock helps us to figure out how old species are, even without fossils. The blue bars indicate statistical error of these estimates.

The molecular clock

Intriguingly, mutations arise at an approximately constant rate. This phenomenon, known as the molecular clock, helps us to infer how long ago two species had a common ancestor and thus how old they are – very useful for invertebrate animals that rarely fossilise! The gene 16S in the example above is found in all insects and accumulates changes at the rate of about 1 DNA base (1 position in sequence) out of a hundred every million years. Finding 20 differences per 100 bases between Heliconius melpomene and Heliconius erato suggests that the two species diverged approximately 10 Million years ago: 10 independent mutations on each branch, one mutation per Million years. Of course, the clock is not perfect and the rate varies between lineages of life – advanced statistical techniques and sequencing large amounts of DNA are needed to get precise estimates.

Figure 3. The molecular clock – the time that passed between past events (like speciation) and today corresponds to the amount of changes accumulated in DNA (red ticks). We find that H. melpomene and H. cydno are more closely related to each other than to H. erato, and that they split about 3 million years ago.

Genes and hybridisation

Heliconius butterflies of different species occasionally exchange adaptive genes, just like modern humans and Neanderthals did. But how can we actually know this without travelling back in time?

If two species do not mix and we compare their genome sequences like in Figure 1, every part of their genome should have the same history. But if some genes were transferred between species, we can expect an unusual pattern of DNA sequences. For example, the warning pattern gene in the Heliconius elevatus genome is unexpectedly closely related to the gene from H. melpomene, suggesting that the sequences were transmitted from H. melpomene to H. elevatus. Such transfer is possible through rare hybridisation, and it is enhanced if the shared genes confer an adaptive advantage of anti-predator warning.

Other applications of phylogenetics

The only illustration in Charles Darwin’s “Origin of Species” is in fact a tree of relations between hypothetical organisms. The modern ability to figure out the relations between DNA sequences is immensely useful in other areas of research. For example, we can use phylogenetic trees to establish where the pandemics of flu and other diseases originate, to show that pathogenic strains of bacteria share the genes for antibiotic resistance, or – in a very famous criminal case – when and where someone got infected with HIV! The same reasoning has also helped us understand that all human populations originated in Africa and how we spread across the globe. If only Darwin new how big the trees will grow!

Krzysztof M. Kozak was raised in Poland and studied in the USA. A bird-watchig trip to Costa Rica and a failed organic synthesis exam convinced him to become an evolutionary biologist rather than a biochemist. Seven years and several trips to the tropics later, he is a happy graduate student at Cambridge, always looking for more ways to combine fieldwork, genetics and computation to understand the tremendous diversity of life. #KrzysztofMKozak

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